PDB-30ju: X-ray structure of lysozyme treated with V(V)-lactate complex (st...

ID or keywords:

Entry

Database: PDB / ID: 30ju

Title

X-ray structure of lysozyme treated with V(V)-lactate complex (structure B)

Components

Lysozyme C

Keywords

HYDROLASE / protein metalation

Function / homology

Function and homology information

Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium ...
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.355 Å

Authors

Paolillo, M. / Ferraro, G. / Merlino, A.

Funding support

Italy, 1items

Citation

Journal: Inorg.Chem. / Year: 2026
Title: Speciation, Protein Binding, Biotransformation, and Cytotoxicity of a VV-Lactate Complex.
Authors: Paolillo, M. / Cuomo, V. / Ferraro, G. / Imbimbo, P. / Gumerova, N.I. / Pisanu, F. / Garribba, E. / Rompel, A. / Merlino, A.

History

Deposition	Apr 29, 2026	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 30, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	30ju.cif.gz	49.8 KB	Display	PDBx/mmCIF format
PDB format	pdb30ju.ent.gz		Display	PDB format
PDBx/mmJSON format	30ju.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/0j/30ju ftp://data.pdbj.org/pub/pdb/validation_reports/0j/30ju	HTTPS FTP

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Related structure data

Related structure data	30jsC 30jxC 30jyC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (3) #136 - Apr 2011 Nanobodies similarity (3) #222 - Jun 2018 Proteins and Nanoparticles similarity (3) #9 - Sep 2000 Lysozyme similarity (3) #142 - Oct 2011 PDB Pioneers similarity (3)

Deposited unit

AAA: Lysozyme C

hetero molecules

15.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	78.225, 78.225, 37.677
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	AAA-348- HOH
2	1	AAA-376- HOH
3	1	AAA-441- HOH
4	1	AAA-450- HOH
5	1	AAA-454- HOH

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Protein , 1 types, 1 molecules AAA

#1: Protein	Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 7 types, 162 molecules

#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO₃
#5: Chemical	ChemComp-A1J6Z / Cyclic trivanadate / 2,4,6-tris(oxidanyl)-1,3,5-trioxa-2$l^{5},4$l^{5},6$l^{5}-trivanadacyclohexane 2,4,6-trioxide Mass: 299.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₃O₉V₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-VVB / bis(oxidanyl)vanadium Mass: 84.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₂O₂V / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-A1J6T / Dioxidovanadium(V) lactate complex / (5~{S},10~{S})-5,10-dimethyl-2,2,7,7-tetrakis(oxidanylidene)-1$l^{3},3,6$l^{3},8-tetraoxa-2$l^{7},7$l^{7}-divanadatricyclo[5.3.0.0^{2,6}]decane-4,9-dione Mass: 342.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₁₀V₂ / Feature type: SUBJECT OF INVESTIGATION
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.01 Å³/Da / Density % sol: 38.83 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 20% ethylene glycol, 0.6 M sodium nitrate, 0.1 M sodium acetate pH 4.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87313 Å
Detector	Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 14, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 1.34→55.31 Å / Num. obs: 25659 / % possible obs: 100 % / Redundancy: 11.8 % / CC_1/2: 0.998 / Net I/σ(I): 7.8
Reflection shell	Resolution: 1.34→1.37 Å / Num. unique obs: 1243 / CC_1/2: 0.378

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.355→55.31 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.951 / SU B: 1.254 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.067 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2166	1164	4.942 %
R_work	0.1745	22388	-
all	0.177	-	-
obs	-	23552	90.696 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 20.786 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.013 Å²	0 Å²	0 Å²
2-	-	-0.013 Å²	0 Å²
3-	-	-	0.027 Å²

Refinement step

Cycle: LAST / Resolution: 1.355→55.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1001	0	50	154	1205

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	1134
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.014	1013
X-RAY DIFFRACTION	r_angle_refined_deg	1.92	1.686	1547
X-RAY DIFFRACTION	r_angle_other_deg	1.552	1.599	2311
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.583	5	138
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.161	20.441	68
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.567	15	184
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.696	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	137
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	1324
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	306
X-RAY DIFFRACTION	r_nbd_refined	0.254	0.2	262
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	923
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	527
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	466
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.23	0.2	72
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.076	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.033	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.145	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.232	0.2	41
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.171	0.2	34
X-RAY DIFFRACTION	r_mcbond_it	1.878	1.836	541
X-RAY DIFFRACTION	r_mcbond_other	1.854	1.829	539
X-RAY DIFFRACTION	r_mcangle_it	2.63	2.751	682
X-RAY DIFFRACTION	r_mcangle_other	2.634	2.757	683
X-RAY DIFFRACTION	r_scbond_it	3.009	2.256	592
X-RAY DIFFRACTION	r_scbond_other	2.99	2.233	573
X-RAY DIFFRACTION	r_scangle_it	4.562	3.271	864
X-RAY DIFFRACTION	r_scangle_other	4.511	3.224	830
X-RAY DIFFRACTION	r_lrange_it	6.073	22.966	1340
X-RAY DIFFRACTION	r_lrange_other	5.959	22.402	1314

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.355-1.39	0.285	25	0.355	418	X-RAY DIFFRACTION	23.4889
1.39-1.429	0.355	50	0.327	919	X-RAY DIFFRACTION	52.9508
1.429-1.47	0.316	87	0.306	1592	X-RAY DIFFRACTION	94.22
1.47-1.515	0.287	94	0.243	1642	X-RAY DIFFRACTION	100
1.515-1.565	0.254	81	0.219	1611	X-RAY DIFFRACTION	100
1.565-1.62	0.224	81	0.196	1542	X-RAY DIFFRACTION	100
1.62-1.681	0.231	77	0.18	1503	X-RAY DIFFRACTION	100
1.681-1.749	0.228	75	0.183	1457	X-RAY DIFFRACTION	100
1.749-1.827	0.201	77	0.18	1383	X-RAY DIFFRACTION	100
1.827-1.916	0.225	76	0.18	1326	X-RAY DIFFRACTION	100
1.916-2.02	0.189	58	0.165	1287	X-RAY DIFFRACTION	100
2.02-2.142	0.195	59	0.164	1202	X-RAY DIFFRACTION	100
2.142-2.29	0.219	53	0.165	1157	X-RAY DIFFRACTION	100
2.29-2.473	0.212	59	0.158	1062	X-RAY DIFFRACTION	100
2.473-2.708	0.18	52	0.155	990	X-RAY DIFFRACTION	99.9041
2.708-3.027	0.221	43	0.163	894	X-RAY DIFFRACTION	100
3.027-3.493	0.212	43	0.153	806	X-RAY DIFFRACTION	99.8824
3.493-4.274	0.184	32	0.14	696	X-RAY DIFFRACTION	100
4.274-6.027	0.21	32	0.171	553	X-RAY DIFFRACTION	100
6.027-55.31	0.339	10	0.253	348	X-RAY DIFFRACTION	100

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Protein , 1 types, 1 molecules AAA

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